AD
Data & Repro
Adaptyv
Adaptyv is a cloud laboratory platform that provides automated protein testing and validation services. Submit protein sequences via API or…
K-Dense-AI/claude-scientific-skillsView
Data & Repro
BI
binder-design
Maintainer FreedomIntelligence · Last updated April 1, 2026
Guidance for choosing the right protein binder design tool. Use this skill when: (1) Deciding between BoltzGen, BindCraft, or RFdiffusion, (2) Planning a binder design campaign, (3) Understanding trade-offs between different approaches, (4) Selecting tools for specific target types. For specific tool parameters, use the individual tool skills (boltzgen, bindcraft, rfdiffusion, etc.).
Original source
FreedomIntelligence/OpenClaw-Medical-Skills
https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/binder-design
- Maintainer
- FreedomIntelligence
- License
- MIT
- Last updated
- April 1, 2026
Skill Snapshot
Key Details From SKILL.md
Key Notes
- Trim to binding region + 10A buffer.
- Remove waters and ligands.
- Renumber chains if needed.
- Trim to binding region + 10A buffer Remove waters and ligands Renumber chains if needed.
- modal run modal_rfdiffusion.py \ --pdb target.pdb \ --contigs "A1-150/0 70-100" \ --hotspot "A45,A67,A89" \ --num-designs 500.
Source Doc
Excerpt From SKILL.md
Tool comparison
| Tool | Strengths | Weaknesses | Best For |
|---|---|---|---|
| BoltzGen | All-atom, single-step, ligand-aware | Higher GPU requirement | Standard (recommended) |
| BindCraft | End-to-end, built-in AF2 validation | Less diverse | Production campaigns |
| RFdiffusion | High diversity, fast | Requires ProteinMPNN | Exploration, diversity |
| Germinal | Nanobody/VHH design | Specialized | Antibody optimization |
Recommended Pipeline: BoltzGen → Chai → QC
BoltzGen provides all-atom design with built-in side-chain packing:
2. Hotspot selection
- Choose 3-6 exposed residues
- Prefer charged/aromatic residues
- Cluster spatially (within 10-15A)
Use cases
- Use binder-design in research workflows aligned with this subject area.
- Follow the upstream documentation for the full working procedure.
Not for
- Do not rely on this catalog entry alone for installation or maintenance details.
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